We are studying the effect of an inhibitor of the cGAS-STING signaling pathway H151 on T-ALL model cell line Jurkat.
The biological experiment revealed that H151 causes cell death, so the pathway is important for survival of T-ALL.
We want to explore the differential expressed genes between normal condition and by inhibiting the pathway. Thus we are going to perform a differential expression analysis (DEA) followed by a pathway enrichment analysis (PEA)
Following a basic RNA-seq pipeline analysis
First let’s view the distribution of the different bio types we have in our data :
In the downstream analysis (DEA),
we’ll be focusing on the top 2 biotypes (protein_coding and
lncRNA). Additional filtering will be applied :
MaxCount_threshold = 20 (At least 1
sample must have a read count over that value)CpmCount_threshold = 0.5 (Count per
million reads threshold)MinSample = 3 (Samples that should
pass the cpm threshold)Now to understand the global gene expression landscape and to assess the quality control of our data, we need to perform a dimentionality reduction analysis : Principal component analysis (PCA)
The PCA :
So we need to perform some data transformation first on
raw counts.
We’ll be using a Variance Stabilizing
Transformation (VST) from the DESeq2 package. And
This will :
DESeq2 computes size
factors using a median-of-ratios method)Now let’s dive into gene expression.
dds <- pre_process_results$DESeqData
dds$Condition <- relevel(dds$Condition, ref = "Jurkat_ct") ## set the control
dds <- DESeq(dds) Let’s get a quick overview of the distribution of the DEGs
DEGs list overview
## [1] "MIR210HG" "ENSG00000288930" "CXCR3" "APLN"
## [5] "H2BC21" "RANBP3-DT" "RGS6" "IRAIN"
## [9] "ENSG00000196465" "BHLHE40" "ENSG00000181577" "ENSG00000146223"
## [13] "COL6A3" "LINC00484" "ENSG00000125651" "VGF"
## [17] "SLAMF8" "KANK4" "ENSG00000211454" "WNT8B"
## [21] "TMEM240" "ENSG00000236204" "MSLNL" "ENSG00000213139"
## [25] "TMEM163" "NANOS1" "LINC01963" "ENSG00000170571"
## [29] "RPRML" "ENSG00000086300" "ENSG00000136840" "CCR8"
## [33] "ENSG00000290124" "KIT" "ENSG00000269968" "ENSG00000230148"
## [37] "TMEM269" "ILF3-DT" "ENSG00000173914" "TERT"
## [41] "CLEC12A" "ENSG00000171357" "ENSG00000138614" "PKD1P6-NPIPP1"
## [45] "RNASEH2A" "DTL" "ENSG00000261226" "UNG"
## [49] "ENSG00000183979" "ENSG00000165028" "ENSG00000182197" "ASH1L-AS1"
## [53] "ENSG00000205903" "MCM4" "TOLLIP-DT" "MIF4GD-DT"
## [57] "ENSG00000272356" "ZNF674-AS1" "ENSG00000198034" "TCHH"
## [61] "LVRN" "ENSG00000143971" "YTHDF3-DT" "ENSG00000287362"
## [65] "ENSG00000277767" "GPR146" "ENSG00000289128" "FAM30A"
## [69] "ENSG00000233178" "ENSG00000276390" "ENSG00000187164" "ENSG00000142556"
## [73] "CXXC4" "ENSG00000124370" "REEP1" "LRRC10B"
## [77] "DDIT4" "ENSG00000167863" "H4C9" "ENSG00000224066"
## [81] "ENSG00000151093" "ENSG00000165475" "C16orf95-DT" "TINCR"
## [85] "ENSG00000289985" "ZNF346-IT1" "DDT" "ENSG00000259736"
## [89] "SCLY" "ENSG00000288586" "HERC3" "PTPN6"
## [93] "ENSG00000278611" "SLC37A2" "ENSG00000140092" "ENSG00000231527"
## [97] "TRARG1" "DENND2D" "TMEM255B" "FOXD2-AS1"
## [101] "LINC00641" "LRRC8D-DT" "NIPBL-DT" "ENSG00000138738"
## [105] "PCNA" "ENSG00000251247" "ENSG00000183891" "ENSG00000163935"
## [109] "GET1" "MYT1L" "UHRF1" "C1S"
## [113] "PRKCZ-AS1" "SLFNL1-AS1" "ENSG00000137941" "SLC16A4-AS1"
## [117] "ELFN2" "FAM81A" "SASH3" "ZNF710-AS1"
## [121] "JAKMIP1" "MAD2L1-DT" "ENSG00000260442" "TWIST1"
## [125] "ABTB3" "ENSG00000244184" "ADGRL2" "GJD3-AS1"
## [129] "MYO18B" "TBC1D22A-DT" "ENSG00000157800" "ENSG00000126107"
## [133] "ENSG00000102409" "MHENCR" "CSPG5" "LNP1"
## [137] "GNA15" "ENSG00000197548" "ENSG00000133794" "MCM2"
## [141] "SNHG10" "P2RX6" "FA2H" "MCM3"
## [145] "C9orf163" "ENSG00000175040" "OPN3" "ENSG00000143740"
## [149] "SLBP" "NECAB3" "ENSG00000105808" "RASSF1-AS1"
## [153] "ENSG00000178982" "ENSG00000185621" "PDK1-AS1" "ENSG00000291056"
## [157] "SUGT1-DT" "ENSG00000124140" "LINC01311" "ENSG00000285437"
## [161] "EID2B" "ENSG00000100003" "PDE4A" "MCM7"
## [165] "NKILA" "IGLL1" "ENSG00000243479" "ENSG00000100321"
## [169] "NOTCH1" "ENSG00000287104" "ENSG00000158555" "PPM1H"
## [173] "ENSG00000153936" "PDXP" "MCPH1-DT" "RNF139-DT"
## [177] "ENSG00000173218" "ENSG00000155366" "ENSG00000267757" "ENSG00000055950"
## [181] "ENSG00000162413" "JMJD7" "MCF2L-AS1" "ENSG00000246308"
## [185] "ENSG00000065413" "DTX1" "CALML4" "FEN1"
## [189] "ENSG00000113595" "RMI2" "LINC01284" "ENSG00000139266"
## [193] "KRT72" "HK2" "ENSG00000153561" "GNMT"
## [197] "ENSG00000118242" "GABPB1-IT1" "TCF7" "PIGW"
## [201] "CIRBP-AS1" "ATP2B2" "IMPDH2" "ZNF704"
## [205] "ENSG00000267688" "ENSG00000114019" "H3C10" "LINC01971"
## [209] "OXTR" "ENSG00000068394" "ENSG00000185885" "PARTICL"
## [213] "PANO1" "LINC00235" "MIR193BHG" "FBXL22"
## [217] "ST3GAL1-DT" "ENSG00000196810" "TTC7A" "NT5DC2"
## [221] "POLG" "ENSG00000286548" "ENSG00000006194" "NPIPB13"
## [225] "PAXIP1-DT" "ANKRD37" "NUP210" "ENSG00000106336"
## [229] "LINC00528" "CNN3-DT" "WT1" "ENSG00000198353"
## [233] "ZMYND19" "ENSG00000108479" "PRKCH-AS1" "ENSG00000221823"
## [237] "ENSG00000165915" "ENSG00000160867" "LINC02019" "YEATS2-AS1"
## [241] "RHPN2" "CXXC5" "NCBP2AS2" "STAM-DT"
## [245] "ENSG00000104219" "LINC00304" "NPIPB11" "RORB-AS1"
## [249] "ENSG00000149823" "LINC01422" "ENSG00000177556" "GNG4"
## [253] "DNAH10OS" "NOTCH2NLB" "LINC01389" "ENSG00000101336"
## [257] "ENSG00000276853" "ENSG00000213047" "LINC02918" "DANCR"
## [261] "IVNS1ABP"
## [1] "CEP126" "ZNF836" "SLC26A11" "CLEC18B"
## [5] "PCDHGA6" "SLC8A2" "PLCD1" "RNFT1"
## [9] "RAP2C-AS1" "RELB" "DDX19A-DT" "ZBTB7B"
## [13] "SP2-DT" "ANKRD31" "PCYT1B" "ENSG00000204482"
## [17] "LINC01058" "MACO1" "LINC00652" "LINC01134"
## [21] "LINC01215" "LINC-PINT" "USP27X-DT" "NQO2"
## [25] "NIPAL1" "PLTP" "ZNF585B" "NPIPA5"
## [29] "STPG1" "ENSG00000289958" "RPAP3-DT" "DMGDH"
## [33] "CFAP69" "ZNF329" "APOBEC3G" "CLIC4"
## [37] "C2orf50" "ENSG00000138061" "SERPINI1" "ENSG00000272438"
## [41] "B3GNT5" "PLEKHA6" "GDPD1" "MAP1A"
## [45] "GABRB2" "DUSP16" "ERCC6L2-AS1" "CCT6B"
## [49] "GARIN1A" "ACTRT3" "ELL2" "BCHE"
## [53] "SHF" "TCP11L2" "ARMH4" "TMEM79"
## [57] "TSPAN10" "PCAT1" "ENSG00000102245" "PEX5L"
## [61] "SNRPA1-DT" "ACTR3-AS1" "MYO5B" "TBC1D30"
## [65] "FGF22" "ENSG00000261173" "LINC01115" "RGPD3"
## [69] "ANG" "SPRY3" "IFI35" "CPEB1-AS1"
## [73] "DOK4" "ENSG00000177788" "IFRD1" "PRDM8-AS1"
## [77] "MIR4280HG" "CASP9" "LINC00662" "CNGA1"
## [81] "SPTB" "ZNF610" "C3AR1" "ENSG00000291010"
## [85] "PCDHGA10" "ERRFI1" "TWF2-DT" "FRRS1"
## [89] "TNS2" "MPZL3" "TSNAXIP1" "EGFL7"
## [93] "RORA-AS1" "ENSG00000178896" "SCG2" "COPB2-DT"
## [97] "ZNF225-AS1" "SLC16A9" "DENND2C" "RSPH4A"
## [101] "ENSG00000197024" "LNCRNA-IUR" "LINC01465" "SLC17A7"
## [105] "FZD7" "MCTP1" "HOXB6" "WNK4"
## [109] "RAB39B" "NUDT13" "LRP12" "LINC00853"
## [113] "CYP2J2" "WDR31" "MIR4435-2HG" "CTSG"
## [117] "ENSG00000105698" "ENSG00000213588" "ID1" "ENSG00000213465"
## [121] "SLCO3A1" "SYNE4" "CD84" "SLC38A3"
## [125] "FAM219A" "CYSRT1" "SERTAD1" "DNAAF8"
## [129] "LAT2" "CA13" "DNAJC3" "TNN"
## [133] "ERBB2" "CAPS" "JAM2" "ULBP2"
## [137] "RXRA" "FAM174A-DT" "FLVCR2" "ZNF451-AS1"
## [141] "LINC02709" "PILRA" "C11orf65" "HDAC2-AS2"
## [145] "SPNS3" "ENSG00000260874" "ICOS" "CBS"
## [149] "ENSG00000125775" "PCOTH" "EVI2A" "RTN2"
## [153] "ADAM8" "IL20RB" "BAZ2B-AS1" "BEND6"
## [157] "FTH1" "TMEM151A" "TMEM267" "GCNT4"
## [161] "PEX11G" "C19orf38" "BTG1-DT" "DNAI7"
## [165] "DDRGK1" "CCDC184" "P2RY10" "ENSG00000228436"
## [169] "SDCBP2-AS1" "TMBIM1" "ENSG00000140104" "OASL"
## [173] "FOSB" "DBNDD1" "CCDC69" "NECTIN3"
## [177] "ENSG00000108599" "JAML" "ENSG00000275793" "TMEM254-AS1"
## [181] "ENSG00000285706" "IRAK2" "EFNB2" "ENSG00000288996"
## [185] "TAGLN" "HULC" "BVES" "SYNGR4"
## [189] "CACNG8" "ALG1L9P" "CCNB3" "FMO4"
## [193] "PEAR1" "SLC43A1" "MIA2" "ZFAND2A-DT"
## [197] "RAB17" "LINC01825" "CDS1" "EVA1B"
## [201] "TPST1" "RPL37A-DT" "CYB5R1" "C14orf39"
## [205] "NES" "APOL1" "SSC4D" "TXNRD1"
## [209] "C22orf23" "METTL27" "EHD2" "SAMD12-AS1"
## [213] "PDGFRL" "MAML2" "ZNF235" "GAB2"
## [217] "CGRRF1" "DAPP1" "LCA5L" "ENSG00000162543"
## [221] "DNAJB9" "IRAG2" "CCDC65" "GPT2"
## [225] "SLC9A9" "LINC00877" "WIPI1" "EPHX1"
## [229] "LYPLAL1-DT" "MN1" "MKLN1-AS" "BTG2-DT"
## [233] "ENSG00000188761" "SEL1L3" "ENSG00000283141" "NUTM2E"
## [237] "RBP5" "BBC3" "EPS8" "NEK5"
## [241] "ASS1" "ECE1-AS1" "ARHGAP29" "RGS17"
## [245] "EIF4EBP1" "ABHD3" "TXK" "EID3"
## [249] "DLGAP1-AS2" "CTSO" "WEE2-AS1" "ENSG00000021574"
## [253] "PGGHG" "ACTN2" "BMP10" "OXR1-AS1"
## [257] "KIF5C" "CYP1A1" "MFAP3L" "LINC00680"
## [261] "TRIM22" "LAMC3" "ZFP2" "ENSG00000289183"
## [265] "ZNF582" "ENSG00000273183" "PCLO" "PLEKHH3"
## [269] "SPOPL-DT" "EAF2" "LINC02901" "LGALS8-AS1"
## [273] "NAGS" "ATF3" "HSPA5" "HABP2"
## [277] "GCLM" "FBXO38-DT" "HERPUD1" "IL23A"
## [281] "TIAM2" "TM6SF1" "DLL1" "LINC01694"
## [285] "ADGRB1" "SLC2A12" "ENSG00000102543" "LINC00659"
## [289] "TLR3" "TLR5" "DGKG" "ASNS"
## [293] "NKX2-2" "FAM43A" "IL15RA" "PTGER3"
## [297] "ENSG00000204356" "CDKN1A" "C7orf31" "FAAH2"
## [301] "TFE3" "ABHD4" "ENSG00000198752" "SLC48A1"
## [305] "IRF7" "HRH1" "AMIGO2" "MIR22HG"
## [309] "LINC00511" "ENSG00000243811" "AARD" "LINC00239"
## [313] "CILP2" "PCK2" "SMPDL3B" "LINC00882"
## [317] "DMRTA2" "TNFSF9" "UBXN8" "PSAT1"
## [321] "NPAS1" "ENSG00000214770" "CECR2" "ENSG00000291136"
## [325] "EFNA1" "ENTPD1" "SLC12A5-AS1" "PLCL1"
## [329] "CD55" "PRG4" "ENSG00000120071" "SV2B"
## [333] "CREB3L3" "MAGOH-DT" "MIAT" "REPS2"
## [337] "ETFBKMT" "YWHAH-AS1" "KRT10-AS1" "ENO1-AS1"
## [341] "LINC00685" "LINC01277" "ISG20" "PPFIBP2"
## [345] "INCA1" "TMOD1" "ENSG00000291027" "ARRDC3"
## [349] "SYT1" "SLC1A5" "SESN2" "YPEL4"
## [353] "ULBP1" "HRK" "KDSR-DT" "PPP2R3A"
## [357] "FRMD3" "TCAF2" "ENSG00000006634" "NOS1AP"
## [361] "DRC3" "RBM11" "ENSG00000160703" "SNAI1"
## [365] "POF1B" "TTTY14" "SMTNL2" "NCF2"
## [369] "ZNF880" "NCAM1" "TMEM200A" "LY9"
## [373] "LINC02265" "IQUB" "MT1F" "DRAM1"
## [377] "SMOX" "CLIP2" "CEBPB" "ENSG00000226029"
## [381] "TRPC5OS" "CEBPB-AS1" "ENSG00000159496" "AMOT"
## [385] "FKTN-AS1" "LINC01307" "DAB1" "RASD1"
## [389] "MET" "SGIP1" "PHOSPHO1" "GABARAPL1"
## [393] "NECTIN2" "IL7R" "CCER2" "FUT1"
## [397] "WNT10A" "ZNF516-AS1" "ENSG00000139800" "LACTB2-AS1"
## [401] "ENSG00000289115" "LINC02377" "MYH14" "ZBED3-AS1"
## [405] "NIBAN1" "TMEM217" "PLAU" "ENSG00000214046"
## [409] "MYOM2" "DEPTOR" "PMEL" "FLRT1"
## [413] "SMAD7" "ADGRL3" "PRKG2" "ENSG00000115355"
## [417] "GLS2" "LDB3" "PCDHB14" "MPZ"
## [421] "TMEM156" "ENSG00000161016" "TRAF3IP2" "TLL1"
## [425] "MFAP4" "MAFB" "SLC30A1" "TEX14"
## [429] "LINC00029" "ENSG00000119684" "KANK3" "LPIN3"
## [433] "THEMIS2" "SSC5D" "RPL26L1-AS1" "PRRT3-AS1"
## [437] "SHISA2" "CBR3-AS1" "FMN1" "SCN3A"
## [441] "LACC1" "LPAR4" "JDP2-AS1" "ENSG00000172071"
## [445] "NDUFA4L2" "TMEM74B" "ENSG00000110063" "XKRX"
## [449] "PRMT5-DT" "CDC20B" "HYDIN" "ENSG00000124172"
## [453] "ENSG00000205643" "PCDHGB7" "ENSG00000287808" "TBL1X"
## [457] "ST8SIA6" "SCN3B" "RAD9B" "ADGRE1"
## [461] "STC2" "TLR1" "ENSG00000163794" "GAS1RR"
## [465] "ITGB5" "JDP2" "ENSG00000149451" "NR2F2"
## [469] "CRPPA" "ERBB3" "ENSG00000284308" "CDNF"
## [473] "ANXA3" "GBP2" "CALCRL" "ENSG00000135436"
## [477] "TNFRSF11A" "ZNF703" "CHRNB4" "VLDLR-AS1"
## [481] "ENSG00000227500" "ADM2" "ENSG00000180611" "LINC00992"
## [485] "HSPA12B" "UBQLN1-AS1" "TRPC1" "LMX1B"
## [489] "PTGES" "REXO5" "CATSPERG" "ENSG00000157992"
## [493] "LINC02341" "LINC02018" "PCDHGB6" "NQO1-DT"
## [497] "CREB5" "TEX19" "TGFBR3" "SLC45A1"
## [501] "LINC00648" "COLGALT2" "ENSG00000158406" "SYT11"
## [505] "SH2D6" "PCDH12" "RPS6KA2" "CST7"
## [509] "ENSG00000198888" "DUSP8" "ECI2-DT" "TREML2"
## [513] "ERICH2-DT" "WDR93" "PIFO" "CDH15"
## [517] "TMIE" "HSPA1B" "CEACAM1" "SLC16A6"
## [521] "CCDC148" "ZNF35" "ZFPM2" "CFTR"
## [525] "PCDH19" "SP140" "GPAT3" "PPP1R15A"
## [529] "FBXO39" "CXCL3" "TRAT1" "SLC3A2"
## [533] "SORBS1" "MTTP" "KIF17" "ADTRP"
## [537] "ZBTB46" "RGS16" "PIWIL4" "FLRT3"
## [541] "JAKMIP2" "TMEM140" "SPTA1" "CSTA"
## [545] "TC2N" "SCN4B" "PLAC1" "JAKMIP3"
## [549] "FOXA3" "ENSG00000105516" "PRDM1" "HTR2B"
## [553] "F2RL2" "MDN1-AS1" "NQO1" "SOX6"
## [557] "ENSG00000254510" "PATJ" "CHAC1" "LINC02321"
## [561] "HIPK1-AS1" "GPR18" "ENSG00000196132" "FAM166B"
## [565] "CRB3" "MKX" "TLR6" "SCN4A"
## [569] "CLCA1" "LY96" "ENSG00000188739" "IL31RA"
## [573] "NYAP1" "PRPF19-DT" "DPP4" "TRPM6"
## [577] "CCPG1" "AKR1C3" "TRPS1" "CEACAM21"
## [581] "IL12A" "ID2" "OLAH" "MAP3K8"
## [585] "ENSG00000171735" "GLIPR1" "TRIB3" "STYK1"
## [589] "PCDH10-DT" "MATN4" "ENSG00000219200" "BEST1"
## [593] "CCDC110" "TSC22D3" "KCNN3" "FAM133A"
## [597] "ENSG00000132005" "CLU" "PDE11A" "ADRA1A"
## [601] "JUN" "CHRNA6" "DDIT3" "LRRC2"
## [605] "HEPH" "ILDR1" "LINC00632" "ROCK1P1"
## [609] "SATL1" "SLC26A4-AS1" "ENSG00000263528" "LUCAT1"
## [613] "ENSG00000272010" "ENSG00000259905" "GPR132" "FOSL1"
## [617] "XKR3" "SLC6A9" "INPP5J" "GPX2"
## [621] "AKR1C8" "ENSG00000163154" "CRIM1" "UEVLD"
## [625] "LINC02561" "STX5-DT" "SLC7A11" "LINC02539"
## [629] "TSPAN19" "L3MBTL2-AS1" "CYP19A1" "PANX2"
## [633] "CD80" "BMP6" "AKR1C2" "OSGIN1"
## [637] "MMP8" "EGF" "ENSG00000290683" "LINC00365"
## [641] "HRG" "GDAP1L1" "ABCC3" "UCP1"
## [645] "HSPA6" "RHOB" "NMRAL2P" "RASSF6"
## [649] "HMOX1" "C4orf17"
Now inspecting the gene biotypes
Let’s inspect the top up and down genes deeper !
NOTE:
For the downstream analysis, only protein_coding genes will
be kept to ensure the significance of the resulting terms!
The top 30 most significant pathways enriched with these DEGs are
## [1] "leukocyte activation"
## [2] "lymphocyte activation"
## [3] "multicellular organismal-level homeostasis"
## [4] "regulation of cell activation"
## [5] "regulation of leukocyte activation"
## [6] "cell-cell adhesion"
## [7] "regulation of leukocyte differentiation"
## [8] "T cell activation"
## [9] "myeloid leukocyte activation"
## [10] "blood vessel morphogenesis"
## [11] "regulation of hemopoiesis"
## [12] "response to endoplasmic reticulum stress"
## [13] "vasculature development"
## [14] "response to lipid"
## [15] "negative regulation of immune system process"
## [16] "regulation of T cell mediated immunity"
## [17] "response to ketone"
## [18] "leukocyte differentiation"
## [19] "integrated stress response signaling"
## [20] "epithelial cell proliferation"
## [21] "blood vessel development"
## [22] "circulatory system process"
## [23] "response to organic cyclic compound"
## [24] "mononuclear cell differentiation"
## [25] "lymphocyte differentiation"
## [26] "endothelial cell migration"
## [27] "response to topologically incorrect protein"
## [28] "angiogenesis"
## [29] "regulation of lymphocyte differentiation"
## [30] "secretion"
The top 30 pathway with the
highest RichFactor (Count per pathway length
ratio)
## [1] "double-strand break repair via break-induced replication"
## [2] "regulation of ferroptosis"
## [3] "regulation of heat generation"
## [4] "detection of molecule of bacterial origin"
## [5] "ferroptosis"
## [6] "DNA strand elongation involved in DNA replication"
## [7] "epithelial cell fate commitment"
## [8] "regulation of IRE1-mediated unfolded protein response"
## [9] "regulation of DNA-templated DNA replication initiation"
## [10] "negative regulation of endoplasmic reticulum unfolded protein response"
## [11] "heat generation"
## [12] "negative regulation of leukocyte chemotaxis"
## [13] "melanin biosynthetic process"
## [14] "melanin metabolic process"
## [15] "secondary metabolite biosynthetic process"
## [16] "integrated stress response signaling"
## [17] "regulation of T cell mediated cytotoxicity"
## [18] "secondary metabolic process"
## [19] "leukocyte activation involved in inflammatory response"
## [20] "negative regulation of chemotaxis"
## [21] "negative regulation of leukocyte migration"
## [22] "T cell mediated cytotoxicity"
## [23] "regulation of T cell mediated immunity"
## [24] "toll-like receptor signaling pathway"
## [25] "endoplasmic reticulum unfolded protein response"
## [26] "female gonad development"
## [27] "development of primary female sexual characteristics"
## [28] "response to unfolded protein"
## [29] "macrophage activation"
## [30] "positive regulation of tumor necrosis factor superfamily cytokine production"
GSEA is a functional class scoring method for
enrichment analysis! It uses the whole set of genes ranked by the chosen
scoring method: in our case, ranked by p.adjust and
logFC values
ranked_genes <- bitr(all_results$ensembl,
fromType = "ENSEMBL",
toType = "ENTREZID",
OrgDb = "org.Hs.eg.db") %>%
dplyr::mutate(ensembl = ENSEMBL) %>%
inner_join(all_results, by = "ensembl") %>%
dplyr::select(ENSEMBL, ENTREZID, Gene_name, padj, log2FoldChange, Gene_biotype) %>%
dplyr::filter(Gene_biotype == "protein_coding",
padj < 0.5,
abs(log2FoldChange) >= 0.1) %>%
dplyr::mutate(padj = padj + 1e-300,
rank = -log10(padj)*sign(log2FoldChange)) %>%
dplyr::group_by(ENTREZID) %>%
dplyr::slice_max(order_by = abs(rank), n = 1, with_ties = FALSE) %>%
ungroup() %>%
dplyr::arrange(desc(rank))
ranked_genes <- setNames(ranked_genes$rank, ranked_genes$ENTREZID)
ranked_genes <- ranked_genes[intersect(names(ranked_genes),
keys(org.Hs.eg.db, keytype = "ENTREZID"))]## [1] "No results found!"